How to make animations of molecular biology processes by 
Ciro Santilli 35 Updated 2025-02-11 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-02-11 +Created 1970-01-01Drew Berry recommends having a look at clarafi.
Official support is abysmal, very focused on MicroPython and their graphical UI.
The setup impossible to achieve as it requires setting up the Yotta, just like the impossible to setup Compile MicroPython code for Micro Bit locally on Ubuntu 22.04 with your own firmware setup.
So we just use github.com/lancaster-university/microbit-samples + github.com/carlosperate/docker-microbit-toolchain:.hex file size for the hello world was 447 kB, much better than the MicroPython hello world downloaded from the website which was about 1.8 MB!
docker pull ghcr.io/carlosperate/microbit-toolchain:latest
git clone https://github.com/lancaster-university/microbit-samples
cd microbit-samples
git checkout 285f9acfb54fce2381339164b6fe5c1a7ebd39d5
# Select a sample, builds one at a time. The default one is the hello world.
cp source/examples/hello-world/* source
# Build and flash.
docker run -v $(pwd):/home --rm ghcr.io/carlosperate/microbit-toolchain:latest yotta build
cp build/bbc-microbit-classic-gcc/source/microbit-samples-combined.hex "/media/$USER/MICROBIT/"If you try it again for a second time from a clean tree, it fails with:presumably because after Yotta died it started using GitHub as a registry... sad. When will people learn. Apparently we were at 5000 API calls per hour. But if you don't clean the tree, you will be just fine.
warning: github rate limit for anonymous requests exceeded: you must log in Association with innovative schools by Ciro Santilli 35 Updated 2025-02-11 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-02-11 +Created 1970-01-01Maybe we should talk to innovative schools, as they might be more open to such use of technology.
Good packaging! Tested on Ubuntu 22.10:This throws a billion exceptions because we didn't start the visdom server, but never mind that.
git clone https://github.com/activatedgeek/LeNet-5
cd LeNet-5
git checkout 95b55a838f9d90536fd3b303cede12cf8b5da47f
virtualenv -p python3 .venv
. .venv/bin/activate
# Their requirements.txt uses >= and some == are incompatible with our Ubuntu.
pip install
Pillow==6.2.0 \
numpy==1.24.2 \
onnx==1.13.1 \
torch==2.0.0 \
torchvision==0.15.1 \
visdom==0.2.4 \
;
time python run.pyThe scrip does a fixed 15 epochs.
Output on P51:
real 2m10.262s
user 11m9.771s
sys 0m26.368sThe run also produces a
lenet.onnx ONNX file, which is pretty neat, and allows us for example to visualize it on Netron:
2021-04 clogged
Pinned article: ourbigbook/introduction-to-the-ourbigbook-project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivative - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. - Internal cross file references done right:
- Infinitely deep tables of contents:
Figure 6. Dynamic article tree with infinitely deep table of contents.Live URL: ourbigbook.com/cirosantilli/chordateDescendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact